danangcrysnanto / bovine_pangenome_graph

Integrate multiple assemblies into a pangenome graph

Hi there 👋

I am Danang and I have extensive experiences working on the bioinformatics of whole genome sequencing data. Currently I am working to apply graph analytic in order to integrate diverse genetic variations into a unified graph-based pangenome. With this, I extended functional genomics analysis to the genomic regions inaccessible with current standard of a linear genome and facilitate integrative multi-omics data analysis and vizualisation.

Skills

• Professional experiences in bioinformatics data analyses, including (but not limited to) Next generation sequencing, transcriptomic, graph-based genomics, genetic variant discovery, and basic genome assembly
• Main programming languages: Bash (Unix/Linux), R/Bioconductor [Statistical analysis], Python [Extensive use], C++ for bioinformatics
• Data science: Tidyverse, Python Data Science (Numpy, Pandas, Jupyter)
• Application development: Shiny, Flask, Plotly
• Computational pipelines: Snakemake
• Reproducible data: Git, Docker
• High Performance Computing (HPC IBM LSF)
• Others: Affinity Designer, Affinity Photo, Ms. Office, VIM, Latex, vscode, Sublime Text